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  • Chemistry  (3)
  • Inorganic and Physical Chemistry  (3)
  • Base Sequence  (1)
  • Chloroplast DNA variation  (1)
  • 1
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    Complete genome sequence of Treponema pallidum, the syphilis spirochete (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-17
    Description: The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fraser, C M -- Norris, S J -- Weinstock, G M -- White, O -- Sutton, G G -- Dodson, R -- Gwinn, M -- Hickey, E K -- Clayton, R -- Ketchum, K A -- Sodergren, E -- Hardham, J M -- McLeod, M P -- Salzberg, S -- Peterson, J -- Khalak, H -- Richardson, D -- Howell, J K -- Chidambaram, M -- Utterback, T -- McDonald, L -- Artiach, P -- Bowman, C -- Cotton, M D -- Fujii, C -- Garland, S -- Hatch, B -- Horst, K -- Roberts, K -- Sandusky, M -- Weidman, J -- Smith, H O -- Venter, J C -- AI31068/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1998 Jul 17;281(5375):375-88.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomic Research, Rockville, MD 20850, USA. tpdb@tigr.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9665876" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Base Sequence ; Borrelia burgdorferi Group/genetics ; Carrier Proteins/genetics/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; DNA Restriction Enzymes/genetics ; Energy Metabolism/genetics ; Genes, Bacterial ; Genes, Regulator ; *Genome, Bacterial ; Heat-Shock Response/genetics ; Lipoproteins/genetics ; Membrane Proteins/genetics ; Molecular Sequence Data ; Movement ; Open Reading Frames ; Oxygen Consumption/genetics ; Protein Biosynthesis ; Recombination, Genetic ; Replication Origin ; *Sequence Analysis, DNA ; Transcription, Genetic ; Treponema pallidum/*genetics/metabolism/pathogenicity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    PAPER CURRENT
  • 2
    Electronic Resource
    Electronic Resource
    Autopolyploidy in Dactylis glomerata L.: further evidence from studies of chloroplast DNA variation (1989)
    Springer
    Theoretical and applied genetics 78 (1989), S. 393-399 
    Details
    ISSN: 1432-2242
    Keywords: Autopolyploidy ; Chloroplast DNA variation ; Dactylis glomerata L. ; Intraspecific evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Chloroplast DNA variation has been used to examine some of the maternal lineages involved in the evolution of the intraspecific polyploid complex, Dactylis glomerata L. Diploid (2x) and tetraploid (4x) individuals were collected from natural populations of the subspecies glomerata (4x), marina (4x) and lusitanica (2x), as well as from sympatric 2x/4x populations of the Galician type. Digestion of their ctDNA with 11 restriction endonucleases revealed enough variation to characterise three ctDNA variants, designated MBMK, MBmK and mBMK. The distribution of these ctDNA variants reflects different stages in their spread among the populations. The MBMK ctDNA variant predominated at both ploidy levels in subspecies glomerata, lusitanica and marina, and in recent tetraploid Galician/glomerata hybrids. The MBmK variant was detected in a single tetraploid individual and probably results from a relatively recent mutation. Fixation of the mBMK minority variant in the diploid and tetraploid Galician populations adds to the evidence concerning the possible origin of the Galician tetraploids. It means that the Galician diploids were maternal ancestors of the tetraploids. This result complements evidence from earlier studies based on morphology or biochemical markers, and reduces the likelihood that the tetraploids arose by hybridisation between an ancient Galician diploid and an alien tetraploid. It is, however, consistent with a true autopolyploid origin of the tetraploids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00265302
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  • 3
    Electronic Resource
    Electronic Resource
    A shock tube study of methyl-methyl reactions between 1200 and 2400 K (1995)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 27 (1995), S. 1179-1196 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The methyl-methyl reaction was studied in a shock tube using uv narrowline laser absorption to measure time-varying concentration profiles of CH3. Methyl radicals were rapidly formed initially by pyrolysis of various precursors, azomethane, ethane, or methyl iodide, dilute in argon. The contributions of the various product channels, C2H6, C2H5 + H, C2H4 + H2, and CH2 + CH4, were examined by varying reactant mixtures and temperature.The measured rate coefficients for recombination to C2H6 between 1200 and 1800 K are accurately fit using the unimolecular rate coefficients reported by Wagner and Wardlaw (1988). The rate coefficient for the C2H5 + H channel was found to be 2.4 (±0.5) × 1013 exp(-6480/T) [cm3/mol-s] between 1570 and 1780 K, and is in agreement with the value reported by Frank and Braun-Unkhoff (1988). No evidence of a contribution by the C2H4 + H2 channel was found in ethane/methane/argon mixtures, although methyl profiles in these mixtures should be particularly sensitive to this channel. An upper limit of approximately 1011 [cm3/mol-s] over the range 1700 to 2200 K was inferred for the rate coefficient of the C2H4 + H2 channel. Between 1800 and 2200 K, methyl radicals are also rapidly removed by CH3 + H ⇒ 1CH2 + H2. In this temperature range, the reverse reaction was found to have a rate coefficient of 1.3 (±0.3) × 1014 [cm3/mol-s], which is 1.8 times the room-temperature value. © 1995 John Wiley & Sons, Inc.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550271205
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  • 4
    Electronic Resource
    Electronic Resource
    Revised values for the rate coefficients of ethane and methane decomposition (1995)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 27 (1995), S. 305-308 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Revised values are given for the rate coefficients of ethane and methane decomposition derived from the laser absorption shock tube measurements performed by Davidson et al. (1992, 1993). This revision results from a reassessment of the methyl absorption coefficient used in the original studies. © 1995 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550270308
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  • 5
    Electronic Resource
    Electronic Resource
    A study of ethane decomposition in a shock tube using laser absorption of CH3 (1993)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 25 (1993), S. 969-982 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rate coefficient for the unimolecular reaction, C2H6 → CH3 + CH3, was measured in reflected shock wave experiments using narrow-linewidth laser absorption of methyl radicals at 216.6 nm. The experiments were conducted in the falloff regime at the conditions 1350 to 2110 K, 0.58 to 4.4 atm, in 50 to 500 ppm C2H6/Ar and 190 ppm C2H6/N2 mixtures. At temperatures below 1500 K, the measured rate coefficients are in good agreement with the expression of Wagner and Wardlaw (1989). Above 1500 K, the measurements fall increasingly below their predictions. © 1993 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550251109
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  • 6
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    Evaluation of joint probability density function models for turbulent nonpremixed combustion with complex chemistry (1996)
    In:  CASI
    Details
    Publication Date: 2016-06-07
    Description: Two types of mixing sub-models are evaluated in connection with a joint-scalar probability density function method for turbulent nonpremixed combustion. Model calculations are made and compared to simulation results for homogeneously distributed methane-air reaction zones mixing and reacting in decaying turbulence within a two-dimensional enclosed domain. The comparison is arranged to ensure that both the simulation and model calculations a) make use of exactly the same chemical mechanism, b) do not involve non-unity Lewis number transport of species, and c) are free from radiation loss. The modified Curl mixing sub-model was found to provide superior predictive accuracy over the simple relaxation-to-mean submodel in the case studied. Accuracy to within 10-20% was found for global means of major species and temperature; however, nitric oxide prediction accuracy was lower and highly dependent on the choice of mixing sub-model. Both mixing submodels were found to produce non-physical mixing behavior for mixture fractions removed from the immediate reaction zone. A suggestion for a further modified Curl mixing sub-model is made in connection with earlier work done in the field.
    Keywords: Inorganic and Physical Chemistry
    Type: Studying Turbulence Using Numerical Simulation Databases; Part 6; 167-186; NASA-TM-111953
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    NASA TECHNICAL REPORTS
  • 7
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    A new methodology to determine kinetic parameters for one- and two-step chemical models (1996)
    In:  CASI
    Details
    Publication Date: 2016-06-07
    Description: In this paper, a new methodology to determine kinetic parameters for simple chemical models and simple transport properties classically used in DNS of premixed combustion is presented. First, a one-dimensional code is utilized to performed steady unstrained laminar methane-air flame in order to verify intrinsic features of laminar flames such as burning velocity and temperature and concentration profiles. Second, the flame response to steady and unsteady strain in the opposed jet configuration is numerically investigated. It appears that for a well determined set of parameters, one- and two-step mechanisms reproduce the extinction limit of a laminar flame submitted to a steady strain. Computations with the GRI-mech mechanism (177 reactions, 39 species) and multicomponent transport properties are used to validate these simplified models. A sensitivity analysis of the preferential diffusion of heat and reactants when the Lewis number is close to unity indicates that the response of the flame to an oscillating strain is very sensitive to this number. As an application of this methodology, the interaction between a two-dimensional vortex pair and a premixed laminar flame is performed by Direct Numerical Simulation (DNS) using the one- and two-step mechanisms. Comparison with the experimental results of Samaniego et al. (1994) shows a significant improvement in the description of the interaction when the two-step model is used.
    Keywords: Inorganic and Physical Chemistry
    Type: Studying Turbulence Using Numerical Simulation Databases; Part 6; 149-166; NASA-TM-111953
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    NASA TECHNICAL REPORTS
  • 8
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    Effect of chemistry and turbulence on NO formation in oxygen-natural gas flames (1996)
    In:  CASI
    Details
    Publication Date: 2016-06-07
    Description: The effects of chemistry and turbulence on NO formation in oxygen-natural turbulent diffusion flames gas flames have been investigated. The chemistry of nitric oxides has been studied numerically in the counterflow configuration. Systematic calculations with the GRI 2.11 mechanism for combustion of methane and NO chemistry were conducted to provide a base case. It was shown that the 'simple' Zeldovich mechanism accounts for more than 75% of N2 consumption in the flame in a range of strain-rates varying between 10 and 1000 s-l. The main shortcomings of this mechanism are: 1) overestimation (15%) of the NO production rate at low strain-rates because it does not capture the reburn due to the hydrocarbon chemistry, and 2) underestimation (25%) of the NO production rate at high strainrates because it ignores NO production through the prompt mechanism. Reburn through the Zeldovich mechanism alone proves to be significant at low strain-rates. A one-step model based on the Zeldovich mechanism and including reburn has been developed. It shows good agreement with the GRI mechanism at low strain-rates but underestimates significantly N2 consumption (about 50%) at high strain-rates. The role of turbulence has been assessed by using an existing 3-D DNS data base of a diffusion flame in decaying turbulence. Two PDF closure models used in practical industrial codes for turbulent NO formation have been tested. A simpler version of the global one-step chemical scheme for NO compared to that developed in this study was used to test the closure assumptions of the PDF models, because the data base could not provide all the necessary ingredients. Despite this simplification, it was possible to demonstrate that the current PDF models for NO overestimate significantly the NO production rate due to the fact that they neglect the correlations between the fluctuations in oxygen concentration and temperature. A single scalar PDF model for temperature that accounts for such correlations based on laminar flame considerations has been developed and showed excellent agreement with the values given by the DNS.
    Keywords: Inorganic and Physical Chemistry
    Type: Studying Turbulence Using Numerical Simulation Databases; Part 6; 187-206; NASA-TM-111953
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